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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Protein Data Bank Entry:

1dlr

2.300 Å

X-ray

1995-01-25

Activity from ChEMBL: What is pChEMBL ?
MinMeanMedianStandard DeviationMaxCount
pChEMBL:7.4208.5007.4801.49010.6003

List of CHEMBLId :

CHEMBL7492


Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Dihydrofolate reductase
ID:DYR_HUMAN
AC:P00374
Organism:Homo sapiens
Reign:Eukaryota
TaxID:9606
EC Number:1.5.1.3


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:28.939
Number of residues:29
Including
Standard Amino Acids: 28
Non Standard Amino Acids: 1
Water Molecules: 0
Cofactors: NDP
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.212489.375

% Hydrophobic% Polar
71.7228.28
According to VolSite

Ligand :
1dlr_1 Structure
HET Code: MXA
Formula: C17H19N5O2
Molecular weight: 325.365 g/mol
DrugBank ID: DB03695
Buried Surface Area:70.41 %
Polar Surface area: 109.17 Å2
Number of
H-Bond Acceptors: 7
H-Bond Donors: 2
Rings: 3
Aromatic rings: 3
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 4

Mass center Coordinates

XYZ
30.503714.661-1.05121


Binding mode :
What is Poseview ?
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Binding mode
BioSolveIT Image generated by PoseView
Protein
Binding Site
Ligand
Interaction pattern
hydrophobic (CA)
aromatic (CZ)
hydrogen bond acceptor (O)
hydrogen bond acceptor/donor (OG)
hydrogen bond donor (N)
positively ionized (NZ)
negatively ionized (OD1)
metal (ZN)

Legend:

Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand

Image generated using PoseView by BioSolveIT
BioSolveIT


LigandProteinInteraction
AtomAtomResidueDistance
(Å)
Angle (°)Type
N4OILE- 72.97175.13H-Bond
(Ligand Donor)
C21CZPHE- 223.370Hydrophobic
C3'CE2PHE- 223.120Hydrophobic
C6CZPHE- 223.280Hydrophobic
N1OE2GLU- 303.47123.1H-Bond
(Ligand Donor)
N1OE1GLU- 302.67152.67H-Bond
(Ligand Donor)
N2OE2GLU- 302.65167.59H-Bond
(Ligand Donor)
N2OE1GLU- 303.31125.79H-Bond
(Ligand Donor)
C4ACBPHE- 344.330Hydrophobic
C5MCE1PHE- 343.920Hydrophobic
C9CE2PHE- 344.40Hydrophobic
DuArDuArPHE- 343.910Aromatic Face/Face
DuArDuArPHE- 343.910Aromatic Face/Face
C5MCG2THR- 564.470Hydrophobic
C21CBSER- 594.080Hydrophobic
C2'CG1ILE- 603.770Hydrophobic
C51CGPRO- 613.490Hydrophobic
C4'CGPRO- 614.370Hydrophobic
N4OVAL- 1153.08133.61H-Bond
(Ligand Donor)
C5MCBVAL- 1154.030Hydrophobic
C5MC4NNDP- 1873.830Hydrophobic
C21C2DNDP- 1873.720Hydrophobic